Burn blister fluid analysis provides an opportunity to non-invasively investigate the biology of the initial response to burn injury; uncover novel diagnostics or prognostics to assist in clinical decision making and enable the identification of new therapeutic approaches to enhance healing. We performed a proteomic analysis of 87 paediatric burn blister fluid samples using liquid chromatography - tandem mass spectrometry with SWATH (data independent) acquisition, which allows for the large scale relative quantification of multiple proteins between samples. The blister fluid proteomes of all samples were compared to the key clinical features of burn depth classification and time-to-reepithelialisation. Both of these clinical parameters are critical for enabling accurate clinical decisions regarding early burn treatment options. Subsequent analyses revealed significant differences in the biochemistry associated with both burn depth and time-to-reepithelialisation. Interestingly, the protein profiles provided evidence of potential clinical misclassification of some burn wounds examined in this study. Importantly, this highlights the utility of diagnostic markers for burn depth and / or prognostic markers of time-to-reepithelialisation. While full-thickness burns are often grafted and superficial-partial thickness burns are often not, it is more difficult to determine if deep-partial thickness burns should be grafted or not. Thus, utilisation of the results of this study could translate to aid in clinical decision making. Overall, this study provides new insights into the early stages of burn wound biology in children and may help with the development of diagnostic or prognostic tools to assist with clinical decisions regarding burn treatment options.